Ok, this is a bit of a complex question. You can use specific primers if you know those particular species are likely to be present in your sample. But this approach won't let you discover all the diversity that may be present, and you risk false negative data. While there are genes conserved in different species groups (e.g. cellulose synthase in plants and cellulose creating protists), there will be sequence diversity in the genes themselves, so you aren't guaranteed to amplify them from all individual variants.

Regular end-point PCR would also work for a simple presence/absence detection as well.

What is your gDNA sample from? Do you have the facilities and resources to sequence the gDNA directly, assemble, and annotate reads?

Hope this helps!

It's genomic DNA in very low concentrations.

My question is more about official lists for targeting species. Of course, there may be problems of specificity, but SANGER sequencing should make it possible to verify the amplified target.

Do you have any software to recommend? Beacon designer? AlleleID ? etc ...

You could try a whole genome amplification approach.

Hi, Angrand, I use qPCR for detecting specific genera using genera specific primers. But detecting species would be a bit difficult. you can go with metagenome targeting whole 16S for species identification.

Thanks